Austrian coach Alexander Pointner, who said Ammann's equipment allowed him to fly further than his rivals and was therefore illegal, had threatened to protest formally if the Swiss jumper used the bindings in Saturday's large hill competition.
In a sign of discord inside the Austrian camp, two top jumpers said they had no problem with Ammann's bindings.
The head of the Swiss ski team said the Austrians were using the binding as an excuse for their underwhelming performances so far. The Austrians have four of the world's top five jumpers but did poorly in the normal hill contest last week.
At the request of the Swiss, FIS equipment controller Jouko Tormaenen examined the bindings on Friday.
"(He) informed the jury members that he had not detected any violation or conflict with existing rules, therefore the jury members unanimously accepted and confirmed this evaluation," FIS race director Walter Hofer said.
Ammann, a double gold medallist from 2002, easily won the normal hill and is a favourite for the large hill.
"I don't think it's personal but the situation is a bit nervous," he said.
Pointner said he had no regrets about raising the issue and denied the protest threat had been aimed at Ammann.
"It is our task to check on such matters so that there is a clear decision, the Olympic Games are held every four years and things should be equal for all athletes," he said.
But speaking separately, two of Pointner's top jumpers made clear they did not share his concerns.
Austrian jumper Thomas Morgenstern - the defending large hill champion - said Ammann's bindings were not an issue.
"He is in really good shape right now and I think he is jumping really perfectly. It's not my decision (to raise this), there are other people who should talk about it," he said.
Asked if the Austrian coach had made a mistake in talking about the bindings, Morgenstern replied: "I don't know."
Team mate Wolfgang Loitzl said Ammann would be the best jumper even without the modified bindings.
The Austrians say Ammann is using a curved metal binding that allows him to increase his aerodynamic profile and so hang in the air longer.
The Swiss say most skiers chose to modify their bindings.
"Everybody's body is a little bit different so we try to adjust from time to time ... the system has been used the last two seasons by other guys, also by those from Austria, so we just probably did it a little bit better," said Ammann.